The sediments of Haidong bay and Macun bay in Dianchi Lakes' experimental area were studied. The sediment column was cut in every 3cm, and the following items are tested, such as total phosphorus, phosphorus species, which include labile phosphate, Fe,Al-P, Ca-P and residual-P, total nitrogen, nitrate nitrogen, nitrite nitrogen, ammonium nitrogen. The results showed that the loads of nitrogen and phosphorus of these two bays increased quickly in recent years. The Fe, Al-P was the largest component in all the P-forms and the content of ammonium nitrogen in these two bays less than that of other lakes. The layer of 9 to 12 centimeters of the two bays was polluted less than the rests. It indicated that these years more and more wastewater was inflow in these two bays. At the same time, the distribution of each testing items showed another low value between 24 to 39 centimeters. So considering feasibility and economic restriction, we can set the 24 - 39 centimeters depth as a dredging layer.